Elgb333, first, i think your taking one instance completely out of place... i literally looked up like 6 different wikis, aside from this one, detailing John's powers to better understand what he is capable off, and none say he can readily remove an individual's magical abilities, so do provide a link to WHEN he took away this Swamp Thing's abilities so i and the rest can see how and under what conditions he did so, because otherwise were just going to call it an exception, as ive seen a lot of his works and ive never seen him perform this feat against another magician or mage, even in dire situations where it would have been quite necesarry.
Second, fighting conceptial BEINGS is not the same as rendering them useless or powerless, so saying he could fight against the effects of a bullet that acts on magic and nullify its effects is erroneous. You are mixing one concept of another.
Thrid, much of John's Arsenal is meant to fighting demons and specific beings, many spells and incantations are specifically targeted at them, so dont add to this fight an ability aimed at demons or monsters and think it should affect Emiya the same way, and as ScarletFirefly very clearly stated, you cant remove the effect of the Origin Bullets.
Also, coming back from the dead dosent mean John wins, this is a fight to see who kills each other, not what happens after. That being said, i still hand this in favor off Emiya due to how effective he is against Mages, John being one.